Background: Standard treatment in BRAFV600E colorectal cancer (CRC) patients has demonstrated an extremely poor prognosis with only little benefits. Interestingly, BRAFV600E CRC has been identified as a subgroup highly epigenetically regulated in its tumorigenesis and maintenance. Our preliminary data demonstrated loss of BET family genes sensitizes BRAFV600E CRC cells to targeted therapies. However, the activity of BET inhibition is unknown in the context of BRAF mutation. Therefore, we investigated the efficacy of BETi combined with standard treatments in BRAFV600E CRC.

Methods: CRISPR-based synthetic lethality screen was conducted using RKO, BRAFV600E CRC cell line. Library containing 355 epigenetic genes was introduced and cells were treated with either DMSO, BRAFi (vemurafenib), or BRAFi/EGFRi (cetuximab). Clonal dropouts under control versus BRAFi or BRAFi/EGFRi lead to identifying top candidate genes potentially synthetic lethal with standard treatments. We further compared the response to targeted therapies between individual BET family (BRD2/3/4) knockout and control BRAFV600E CRC cell lines by XTT or clonogenic assays. Furthermore, BRAFV600E CRC PDX models were treated with vehicle, BETi (iBET151), MEKi (binimetinib), or BETi/MEKi doublet. The efficacy of BETi (zen3694) and BRAFi/EGFRi triplet combination is under investigation. Also, we tested a combination of BETi/MEKi or BETi/BRAFi/EGFRi in the BRAFV600E CRC model with acquired resistance to BRAFi/EGFRi. We assessed treatment response by measuring tumors volume changes for 21 days. For BETi/MEKi combination, RNA-seq and RPPA were performed at 7 days to understand the pharmacodynamics of the combination.

Results: Our negative selection screen confirmed loss of BRD2, one of the BET family members, sensitizes cells to both targeted treatments (p < 0.05). BRD2 or BRD4 KO CRC cell lines have shown growth inhibition with BRAFi or BRAFi/EGFRi treatments compared to control (p <0.05). Intriguingly, the efficacy study showed selective tumor regression under the combination of BETi/MEKi (-39% volume change in best responding model) while the effect of individual treatment was limited. We also identified potential adaptive resistance mechanisms to BETi treatment, associated with upregulation of key oncogenic signaling and cell cycle regulators, such as MAPK signaling, MYC, or E2F targets; which were significantly inhibited when combined with MEKi. Lastly, we found stabilized tumor growth induced by both combinations of BETi/MEKi and BETi/BRAFi/EGFRi in the resistant PDX model compared to targeted treatment alone (p <0.05).

Conclusion: Our data showed combination of BET inhibition improved sensitivity or overcame resistance to standard targeted therapy in BRAFV600E CRC. Overall, our data suggest that combining BETi with MAPK inhibition could be a novel therapeutic solution for BRAFV600E CRC.

Citation Format: Hey Min Lee, Stefania Napolitano, Alexy Sorokin, Melanie N. Woods, Saikat Chowdhury, Jumanah Y. Alshenaifi, Anand K. Singh, John Paul Shen, Funda Meric-Bernstam, Kunal Rai, Scott Kopetz. Bromodomain and extraterminal (BET) protein inhibition sensitize BRAFV600E colorectal cancer to standard targeted therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3275.